Origin, Evolution, and Virulence of Porcine Deltacoronaviruses in the United States

Ma, Yuanmei; Zhang, Yu; Liang, Xueya; Lou, Fangfei; Oglesbee, Michael; Krakowka, Steven; Li, Jianrong

Unique genetic features of the emergent PdCV strains in the United States. To date, there are eleven complete genomic sequences of U.S. PdCVs available in GenBank. The genome sizes (25,422 nt) of all U.S. PdCV strains are identical. The genomic sequence of PdCV Ohio CVM1 shares 99.6 to 99.7% identity with other U.S. PdCV isolates and 99.7% homology with a South Korean isolate (see Table S1 in the supplemental material). The South Korean strain shares more homology with U.S. strains than Hong Kong strains. Within U.S. PdCV isolates, PdCV Ohio CVM1 shares the highest identity (99.8%) with the OH1987, PA3148, and IL2768 strains, with only 41-, 52-, and 58-nt differences, respectively, across the entire genome. A total of 94 nt differences, accounting for 14 unique amino acid changes, were found between the U.S. PdCV strains and the two Hong Kong strains. Specifically, 10 amino acids (F1019, I1320, I1414, V1483, I1647, I3120, F5442, V5816, H5871, and E5875) in ORF1ab were found to be unique to the U.S. isolates. In addition, 4 amino acids (V551, I670, S698, and I1016) were found to be unique to the S proteins of all known U.S. isolates. These unique amino acids can potentially serve as genetic markers to discriminate between U.S. and Hong Kong strains. Notably, HKU15-155 has a 1-amino-acid deletion at position 52 in the S protein, whereas all other strains have "N" at this position. Interestingly, all the U.S., Hong Kong, and South Korean strains share 100% identity in the E protein (see Table S1 ). Amino acid sequences of M proteins are identical in all strains, with the exception of an A83P substitution in HKU15-155. Only 3 amino acid differences were found in the NS6 proteins among all PdCV strains.